100% satisfaction guarantee Immediately available after payment Both online and in PDF No strings attached
logo-home
Summary Molecular Biology of the Cell (5234MOBC6Y) partial exam 1+2 $11.07   Add to cart

Summary

Summary Molecular Biology of the Cell (5234MOBC6Y) partial exam 1+2

 37 views  3 purchases
  • Course
  • Institution
  • Book

Complete summary of the Molecular Biology of the Cell course (5234MOBC6Y) from the 1st year of the master in biomedical sciences, UvA, compulsory for all tracks. This summary contains all the information needed for partial exam 1 and 2 (Van der Spek, Stam, and Brul), and includes all the material f...

[Show more]

Preview 4 out of 48  pages

  • Yes
  • November 18, 2023
  • 48
  • 2023/2024
  • Summary
avatar-seller
Molecular Biology of the Cell
summary (exam 1+2)




1

,DNA Replication & Sequencing & PCR 3
Genomes & Omics & Bioinformatics 6
RNA Gene Expression 8
Translation & Protein Degradation 11
Gene Cloning & Manipulation 13
Transgenesis 16
Epigenetics & Chromatin 18
DNA Methylation, Gene Regulation & Genome Stability 20
Histone Modi cations 25
Histone Variants 28
Non-coding RNAs 31
Protein Synthesis, Structure & Puri cation 35
Membranes & Protein Targeting 39
Vesicular Transport 42
Cellular (Stress) Signaling & Cell Division 45




2


fi fi

,DNA Replication & Sequencing & PCR
THE CENTRAL DOGMA
- Going from the gene to function: DNA -> RNA -> protein -> metabolite -> phenotype
- Replication (DNA synthesis): DNA -> DNA
- ~ PCR, sequencing
- Transcription (RNA synthesis): DNA -> RNA
- ~ promoters, regulatory factors, splicing
- Translation (protein synthesis): RNA -> protein (made from amino acids)
- ~ RNA structure and stability, ribosomes, post-translational modi cations (=decoration of
proteins)

DNA SYNTHESIS / REPLICATION
- DNA replication is semi-conservative: every new double-stranded molecule consists of 1 old
and 1 new strand
- The old strand is the template (i.e., example) for the new strand
- 1 parental DNA double helix results in 2 identical daughter DNA double helices
- DNA replication always occurs 5’->3’; the template strand is anti-parallel (3’->5’)
- DNA synthesis is the process of the formation of phosphodiester bonds while hydrolyzing
the matching dNTP (deoxyribonucleoside triphosphate) molecule
- The energy comes from the DNA backbone: as the phosphodiester bond forms between
the 5’ phosphate group of the new nucleotide and the 3’ OH of the last nucleotide, 2
phosphates are removed providing energy for bonding
- DNA polymerase synthesizes DNA from a double-stranded ‘primer’
- DNA polymerase requires a stable primer already bound to the template strand to
synthesize DNA, since it needs a pre-existing 3’ OH to elongate the strand
- The replisome is a molecular machine with essential components for DNA replication:
- Topoisomerase: enzyme that regulates the over-/underwinding of DNA by making a nick
in the DNA, thereby releasing the tension of the coiled DNA helix
- Helicase: breaks hydrogen bonds between DNA strands, thereby separating the strands
using ATP
- Primase: RNA polymerase that synthesizes a short RNA primer that is complementary to
a single-stranded DNA template, which is needed by DNA polymerase
- After elongation of the strand, the primer is removed by a 5’ to 3’ exonuclease and
replaced by DNA
- 2 DNA polymerases: one synthesizes leading strand, while the other synthesizes the
lagging strand
- Leading strand: template (antisense) strand that goes 3’->5’
- Replication occurs continuously 5’->3’
- 1 RNA primer is made at the origin
- Lagging strand: anti-parallel template strand (coding/sense) that goes 5’->3’
- Replication occurs discontinuously 5’->3’
- Many RNA primers are required to synthesize Okazaki fragments (=small 5’->3’
DNA fragments)
- Ligase: covalently links adjacent Okazaki fragments together

MISTAKES IN DNA SYNTHESIS
- Mistakes in DNA synthesis can be restored through ‘proofreading’ activity of the DNA
polymerase complex
- Without proofreading (5’->3’ polymerization): 1 error per 105 nucleotides
- With proofreading: 1 error per 102 nucleotides
- Proofreading: DNA polymerase recognizes a mismatched nucleotide by 3’->5’
proofreading, removes it, replaces it with the correct nucleotide, and allows synthesis
to continue 5’->3’


3


fi

, - With strand-directed mismatch repair: 1 error per 103 nucleotides
- Strand-directed mismatch repair: mismatch proofreading proteins (MutS and MutL)
recognize and bind to an error in newly-made strand -> DNA scanning detects a nick
in new DNA strand -> strand removal containing the error -> repair DNA synthesis
using template
- Occurs after DNA replication
- These 3 mechanisms combined give 1 error per 1010 nucleotides
- If the error would be 0, there would be no evolution: allowing some errors is a good
thing

DNA MUTATIONS
- Chemical changes in DNA bases can cause mutation in the DNA
- Depurination: involves the removal of a purine (G/A) from the DNA, leaving only the sugar
phosphate of the nucleotide
- Results in 1 mutated daughter helix with an A-T/G-C deletion, and 1 unchanged daughter
helix
- Is the most common DNA mutation
- Deamination: involves the removal of an amino group
- Results in 1 mutated daughter helix with a change in base pair, and 1 unchanged daughter
helix
- C -> T
- Deamination of C results in a U -> the mutated daughter strand will have a G to
A conversion in the new strand while U will be repaired into a T -> C to T
conversion at the position of the deaminated C
- A -> G
- G stops replication (stutter/deletion)

DNA SEQUENCING
- DNA sequencing (whole genome) is used to determine the order of the bases A, C, G, and T
- Sanger sequencing / dideoxy sequencing: DNA synthesis while incorporating chain
terminators in separate reaction for the bases A, C, G, and T
- A chain terminator (dideoxynucleotide) lacks the 3’ OH necessary for strand elongation,
thereby preventing extension of the DNA strand, resulting in DNA fragments
- With a high concentration of all dNTPs and low concentrations of ddATP, ddCTP, ddGTP
and ddTTP, in separate reactions DNA synthesis will continue, but occasionally synthesis
will stop when a dideoxynucleotide is incorporated
- The oligonucleotide primer (needed by DNA polymerase) determines the start of the
reaction
- With 4 separate reactions (ddATP/ddCTP/ddGTP/ddTTP + DNA polymerase) and a
labelled (radioactive or uorescent) primer, fragments of di erent lengths are generated:
these fragments are separated alongside using electrophoresis, and every visible fragment
represents a termination in the DNA synthesis
- The DNA sequence is read from the bottom of the gel upward
- E ciency of manual sequencing methods:
- Radioactive nucleotides in 4 lanes: ~8000 bases per day
- Fluorescent nucleotides in 4 lanes: ~10,000 bases per day
- Fluorescent nucleotides in 1 lane: ~30,000 bases per day
- Nucleotides in capillary gel (1-96 wells): ~150,000 bases per day
- Genome sequencing / hierarchical shotgun sequencing: multiple copies of the genome are
randomly fragmented -> the nucleotide sequence of each clone is stitched together, using the
overlaps between clones as a guide
- Works well for small genomes that lack repetitive DNA
- Uses contigs: assembly of smaller DNA sequences into 1 continuous strand
- Needs markers such as restriction enzymes



4


ffi

fl ff

The benefits of buying summaries with Stuvia:

Guaranteed quality through customer reviews

Guaranteed quality through customer reviews

Stuvia customers have reviewed more than 700,000 summaries. This how you know that you are buying the best documents.

Quick and easy check-out

Quick and easy check-out

You can quickly pay through credit card or Stuvia-credit for the summaries. There is no membership needed.

Focus on what matters

Focus on what matters

Your fellow students write the study notes themselves, which is why the documents are always reliable and up-to-date. This ensures you quickly get to the core!

Frequently asked questions

What do I get when I buy this document?

You get a PDF, available immediately after your purchase. The purchased document is accessible anytime, anywhere and indefinitely through your profile.

Satisfaction guarantee: how does it work?

Our satisfaction guarantee ensures that you always find a study document that suits you well. You fill out a form, and our customer service team takes care of the rest.

Who am I buying these notes from?

Stuvia is a marketplace, so you are not buying this document from us, but from seller SummaryLin. Stuvia facilitates payment to the seller.

Will I be stuck with a subscription?

No, you only buy these notes for $11.07. You're not tied to anything after your purchase.

Can Stuvia be trusted?

4.6 stars on Google & Trustpilot (+1000 reviews)

82871 documents were sold in the last 30 days

Founded in 2010, the go-to place to buy study notes for 14 years now

Start selling
$11.07  3x  sold
  • (0)
  Add to cart